Early in the war, Master Zey oversaw the operations on Qiilura where Master Kast Fulier and Padawan Etain Tur-Mukan had gone missing in the confusion surrounding the start of the war. When the commandos of Omega Squad recovered Padawan Tur-Mukan, they assumed the mission of capturing the scientistOvolot Qail Uthan, who planned to develop a nanovirus which would target the clone troopers. When the commandos were successful in capturing Uthan, Master Zey and Padawan Jusik flew to Qiilura to oversee clean-up operations on the world and arm the colonists on the planet to oppose Confederate occupation. Working closely with Jusik and Tur-Mukan, both were raised to the rank of Jedi Knight, and Master Zey strived to reestablish a Gurlanin colony on the world.[1]

Following his successful operation on the planet, Master Zey was placed in charge of one of the two Special Operations Brigades, serving alongside Master Iri Camas as Director of Special Forces. As Master Zey came to rely more and more on the ARC troopers, he was assigned CaptainMaze, who served as liaison between the Special Ops and the ARCs. During this time, Master Zey was informed by his agents that discrepancies were being brought to light regarding the production numbers of Separatist droids. The media and representatives of the Confederacy released numbers which made the army appear to be made up of more than a quadrillion droids; however Zey's Null ARCs had laid their hands on datafiles that set the actual number as less than half a billion. Believing that a planned, large-scale assault on droid production plants could end the conflict, Master Zey took his evidence to the Supreme Chancellor of the Republic; Palpatine dismissed the claims and stated that the use of such excessive force would be unnecessary.[2]

To keep Master Zey occupied, Chancellor Palpatine assigned the Director with capturing the rogue Kaminoan scientist Ko Sai. Tasking Delta Squad and his former Padawan, Jedi Jusik, to find the defector, Zey was unaware that Jusik was purposely throwing his squad off the trail to cover the movements of Kal Skirata. Skirata, one of the many mercenaries who assisted in the initial training of the clones, was also hunting Sai with the assistance of Omega Squad and together they wanted to kill the Kaminoan. Once Sai was captured by Skirata, Jusik and his men discovered the abandoned lab of Ko Sai and deemed her work destroyed. To make the operation see successful, Skirata gave the head of Ko Sai to Delta Squad for them to deliver to Master Zey back on Coruscant.[3]

As the war continued, Master Zey began to feel sympathy for the clones, believing that the Order was wrong to employ men who were bred to fight and had no choice in the matter. To this end, Master Zey offered to find a way to get Captain Maze off Coruscant and into retirement if he ever wanted to leave the military. In addition to the forced lifestyle, Master Zey was mortified when confronted with increasing amounts of evidence pointing to clone executions by the Republic. When this information was brought to light, Master Zey's former Padawan, Jedi Jusik, left the Order, declaring that he could no longer ignore his heart and would protect innocents, including the clones. Sorry to see the man turn to the Mandalorian culture for acceptance, Zey understood Jusik's motives and allowed him to keep his lightsaber.[3]

Assigning Jedi Tur-Mukan and both Delta and Omega Squad to Haurgab, he was not pleased when they returned having reached a stalemate. Approaching clone trainer and mercenary Walon Vau, Master Zey requested that the man keep watch on Kal Skirata, as the man was suspected of treason.[3]

Following the failed invasion of Coruscant by the Confederacy, Master Zey was forced to spend more time at the Jedi Temple as he consulted with the High Council and received reports from other Jedi. On a late night trip to the Temple, Master Zey was walking amongst its halls when Sith LordDarth Vader led the 501st Legion against the Temple. Unbeknownst to the Jedi, Chancellor Palpatine had betrayed the Order, issuing ContingencyOrder 66 to the Grand Army, ordering all Jedi executed. As part of Operation: Knightfall, the 501st stormed the Temple's halls and shot anyone they encountered.[4]

Escaping the burning Temple with severe injuries, Master Zey managed to make it back to his offices at the Special Ops headquarters when he encountered Null ARC Captain Ordo. Asking Ordo why the troopers were killing the Jedi, Ordo told him about Order 66. Captain Maze arrived at this point and told Zey that he was only following orders, and that they had been sent down directly from the Office of the Supreme Chancellor. Realizing what had happened, Master Zey revealed to the clones that Palpatine was indeed the traitor and that he must be the Dark Lord of the Sith, Darth Sidious. Unaware of what a Sith was, Maze pleaded with Zey to allow himself to be arrested and bring these charges forward in front of the Galactic Senate. Refusing to be taken prisoner by the Sith, Zey ordered Maze to follow orders and execute him.[4]

Captain Maze, however, decided not to follow orders, shooting the wall a meter from Zey's head; he then succeeded in hiding Zey until he could smuggle him offworld to Mandalore. Smuggled to Kal Skirata's secret bunker at Kyrimorut, Zey was met with an icy reception; Skirata and his clones hated the Jedi and were angry that the clones had not followed orders. Allowed to stay, the Master met with other Jedi refugees hiding out on the planet, including his former Padawan and the ancient Jedi Kina Ha. Master Zey was surprised when he detected the Force-sensitivity of an infant staying at the bunker. Named Kad, the clones taking refuge there revealed that the boy was the son of the dead Jedi Tur-Mukan and a clone.[5]

Keeping to himself at the bunker, the fates of Masters Zey and Ha were hotly debated by the Mandalorians. Deciding not to execute the two, the Mandalorians were successful at contacting Master Djinn Altis and his hidden community of Jedi, and the Jedi were secretly transported to their secret hiding spot and joined their community.

Zey had to constantly deal with the unorthodox behavior of Kal Skirata and his associates, such as allowing Skirata to use military funds as he needed them, or often turning a blind eye to Generals Bardan Jusik and Etain Tur-Mukan's doings.[4]

Arligan Zey was described as a large bearded, muscular man, uncomfortable with a desk job and the power he wielded, but extremely loyal to the Jedi Order. He was shocked to learn of the execution of clones during the war, and was known to express exasperation over such issues to Mace Windu. He also offered Captain Maze a way out of the army if he ever wanted it.[4]